dsh-molbio-panel 0.1.9 → 0.1.10

package/README.md

@@ -12,12 +12,12 @@ DSH Web GUI 的**浏览器内 Molbio 面板**：右侧栏的一个 tab，列出
 面板必须走 **bundle 渠道**（`dsh.client` 双面包）：preset 渠道挂不了客户端 UI
 （详见 `dsh-molbio-tools` 仓库的 `docs/client-pipeline-exploration.md`）。
 
-而 `dsh-molbio-tools` 的宿主半边会注册 **46 个工具**——把它挂进一个共享的 Web profile，
+而 `dsh-molbio-tools` 的宿主半边会注册 **64 个工具**——把它挂进一个共享的 Web profile，
 等于给**该 profile 的每个会话**都塞进这些工具。所以面板单独成包：
 
 | 包 | 宿主半边 | 用途 |
 | --- | --- | --- |
-| `dsh-molbio-tools` | 46 个 molbio 工具 | 分子生物学专用 profile / preset |
+| `dsh-molbio-tools` | 64 个 molbio 工具 | 分子生物学专用 profile / preset |
 | `dsh-molbio-panel` | **不注册任何工具**（空实现） | 只想在共享 profile 里加一个面板 |
 
 宿主半边刻意保持空：客户端扫描按 **Loader 条目**取包清单，条目只要能加载，浏览器半就能

package/index.mjs

@@ -2,7 +2,7 @@
  * dsh-molbio-panel — host half.
  *
  * This package exists so the browser panel can be installed WITHOUT dragging
- * the 46 molbio tools into every session of a profile. It is a `dsh.client`
+ * the molbio toolset into every session of a profile. It is a `dsh.client`
  * dual-face package: the host half below, and the browser half built from the
  * `dsh-molbio-tools` sources into `lib/client.js`.
  *

package/lib/client.js

@@ -4976,10 +4976,23 @@ window.__ModuleLoader__.load({
 
 			/** Summary statistics over parsed entries. */
 			function entryStats(entries, qualityMode = false) {
-			  const lengths = entries.map((entry) => entry.sequence.length);
+			  // Count in a loop instead of spreading into Math.min/Math.max: a large FASTQ
+			  // can hold hundreds of thousands of reads (and millions of quality
+			  // characters), and spreading such an array overflows the engine's argument
+			  // limit with a RangeError. The numbers are identical; only the failure mode
+			  // changes.
+			  let totalBases = 0;
+			  let minLength = entries.length === 0 ? 0 : Infinity;
+			  let maxLength = 0;
+			  let longest = 0;
 			  let gc = 0;
 			  let at = 0;
 			  for (const entry of entries) {
+			    const length = entry.sequence.length;
+			    totalBases += length;
+			    if (length < minLength) minLength = length;
+			    if (length > maxLength) maxLength = length;
+			    if (length > longest) longest = length;
 			    for (const base of entry.sequence) {
 			      if (base === 'G' || base === 'C') gc++;
 			      else if (base === 'A' || base === 'T') at++;
@@ -4987,22 +5000,34 @@ window.__ModuleLoader__.load({
 			  }
 			  const stats = {
 			    entries: entries.length,
-			    total_bases: lengths.reduce((sum, len) => sum + len, 0),
-			    min_length: Math.min(...lengths),
-			    max_length: Math.max(...lengths),
-			    mean_length: Math.round((lengths.reduce((sum, len) => sum + len, 0) / lengths.length) * 100) / 100,
+			    total_bases: totalBases,
+			    min_length: minLength,
+			    max_length: maxLength,
+			    mean_length: entries.length === 0 ? 0 : Math.round((totalBases / entries.length) * 100) / 100,
 			    gc_percent: gc + at === 0 ? 0 : Math.round((gc / (gc + at)) * 1000) / 10,
 			  };
 			  if (qualityMode) {
-			    const allQ = entries.flatMap((entry) => [...entry.quality].map((ch) => ch.charCodeAt(0) - 33));
-			    if (allQ.length > 0) {
-			      const mean = allQ.reduce((sum, q) => sum + q, 0) / allQ.length;
-			      const low = allQ.filter((q) => q < 20).length / allQ.length;
-			      stats.quality_mean = Math.round(mean * 100) / 100;
-			      stats.quality_min = Math.min(...allQ);
-			      stats.quality_max = Math.max(...allQ);
-			      stats.low_quality_fraction = Math.round(low * 1000) / 1000;
-			      const maxLen = Math.min(150, Math.max(...entries.map((e) => e.sequence.length)));
+			    let qualitySum = 0;
+			    let qualityCount = 0;
+			    let lowCount = 0;
+			    let qualityMin = Infinity;
+			    let qualityMax = -Infinity;
+			    for (const entry of entries) {
+			      for (const ch of entry.quality) {
+			        const q = ch.charCodeAt(0) - 33;
+			        qualitySum += q;
+			        qualityCount++;
+			        if (q < 20) lowCount++;
+			        if (q < qualityMin) qualityMin = q;
+			        if (q > qualityMax) qualityMax = q;
+			      }
+			    }
+			    if (qualityCount > 0) {
+			      stats.quality_mean = Math.round((qualitySum / qualityCount) * 100) / 100;
+			      stats.quality_min = qualityMin;
+			      stats.quality_max = qualityMax;
+			      stats.low_quality_fraction = Math.round((lowCount / qualityCount) * 1000) / 1000;
+			      const maxLen = Math.min(150, longest);
 			      const perPosition = [];
 			      for (let pos = 0; pos < maxLen; pos++) {
 			        const values = entries.filter((e) => e.sequence.length > pos).map((e) => e.quality.charCodeAt(pos) - 33);
@@ -7797,14 +7822,22 @@ window.__ModuleLoader__.load({
 			  }
 			  if (current !== null) peaks.push(current);
 			  const total = points.reduce((sum, point) => sum + point.hydropathy, 0);
+			  // Loop rather than Math.min(...points): the protein length is not capped and
+			  // a long input would overflow the argument limit with a RangeError.
+			  let minimumHydropathy = Infinity;
+			  let maximumHydropathy = -Infinity;
+			  for (const point of points) {
+			    if (point.hydropathy < minimumHydropathy) minimumHydropathy = point.hydropathy;
+			    if (point.hydropathy > maximumHydropathy) maximumHydropathy = point.hydropathy;
+			  }
 			  return {
 			    length: sequence.length,
 			    window,
 			    threshold,
 			    gravy: sequence.length === 0 ? 0 : round2([...sequence].reduce((sum, aa) => sum + KYTE_DOOLITTLE[aa], 0) / sequence.length),
 			    mean_profile: round3(total / points.length),
-			    minimum_hydropathy: round3(Math.min(...points.map((point) => point.hydropathy))),
-			    maximum_hydropathy: round3(Math.max(...points.map((point) => point.hydropathy))),
+			    minimum_hydropathy: round3(minimumHydropathy),
+			    maximum_hydropathy: round3(maximumHydropathy),
 			    peaks: peaks.map((peak) => ({ ...peak, maximum: round3(peak.maximum), length: peak.end - peak.start + 1 })),
 			    points,
 			  };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "dsh-molbio-panel",
-  "version": "0.1.9",
+  "version": "0.1.10",
   "description": "Browser panel for the DeepSeek Harness Web GUI: a Molbio tab in the right sidebar that draws plasmid maps and sequence logos from workspace sequence files, using the same computation modules as the dsh-molbio-tools plugin.",
   "type": "module",
   "main": "index.mjs",